What types of mismatches are supported in `seqkit locate`?

[jeremymsimon]

Hi, could you please clarify what sorts of mismatches are supported in seqkit locate? Is it single base changes only or are insertions and/or deletions allowed as well? fish seems to support indels since the alignment parameters mention gap penalties, is that the preferred tool if I want to include indels?

Thanks!

[shenwei356]

Yes, seqkit locate only supports base mismatches.

[jeremymsimon]

Got it, thanks. And is there documentation on how the MapQual is calculated in fish? I think RawScore is based on the length of the query and the alignment parameters (+4, -4, -2, -1), but I don't see a description of how that relates to the MapQual

[shenwei356]

@botond-sipos might help. He implemented it. :stuck_out_tongue_winking_eye:

[jeremymsimon]

Thanks @shenwei356 @botond-sipos that would be very helpful!